Abstract Spinal cord injury (SCI) disrupts the autonomic nervous system (ANS), impairing the ability of the ANS to coordinate organ function throughout the body. Emerging data indicate that systemic pathology resulting from ANS dysfunction contributes to intraspinal pathology and neurological impairment. For example, the post-injury onset of neurogenic bowel and immune suppression can cause gut dysbiosis ? a pathological state where beneficial symbiotic bacteria (probionts) in the GI tract become outnumbered by aggressive bacteria (pathobionts). Recent data from our lab show that SCI triggers gut dysbiosis, which impairs functional recovery and exacerbates lesion pathology. Since different types of gut bacteria exert unique effects on the host and these effects can vary by sex, it is important to understand how gut ecology changes as a function of time, spinal injury level and injury severity in both males and females. Accordingly, experiments in Aim 1 will use state-of-the-art PhyloChip technology to profile post-SCI changes in gut microbial communities in male and female mice as a function of injury severity, time post-injury and injury level. The primary goal is to identify post-injury changes in gut microbe populations that could be manipulated for therapeutic gain. Gut microbe manipulation is clinically feasible and can profoundly affect mammalian physiology. Indeed, we found that functional recovery is improved and lesion pathology reduced in mice treated post-SCI with a medical-grade probiotic (VSL#3). Aim 2 will explore the mechanisms underlying VSL#3-mediated neuroprotection. SCI can affect the gut microbiome but the altered microbiota can in turn affect the immune system and spinal cord. Aim 3 will examine how SCI-induced gut dysbiosis influences macrophage phenotype and function. Emerging data indicate that gut microbes can cause transcriptional and epigenetic changes in macrophage precursors in bone marrow. Such changes can render mature macrophages more or less responsive to subsequent inflammatory stimuli, including those found in the injured spinal cord. Using germ-free mice (devoid of any commensal microbe) and fecal transplantation to selectively recolonize mice with control or SCI microbiota, we will test whether gut dysbiosis adversely affects macrophage function. Rather than ?treat the spinal cord?, this proposal seeks new ways to treat SCI as a systemic disorder caused by breakdown of the spinal cord-gut-immune axis.